From bbae3808c62fe7b40893c1eb0910bd1757192802 Mon Sep 17 00:00:00 2001
From: Tom Clegg <tom@tomclegg.ca>
Date: Thu, 22 Oct 2020 16:59:24 -0400
Subject: [PATCH] Fix coverage score.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---
 export.go        |  6 +++---
 pipeline_test.go | 14 +++++++-------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/export.go b/export.go
index 42ff4962ad..739f8efa12 100644
--- a/export.go
+++ b/export.go
@@ -321,7 +321,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
 	variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
 	for refstep, libref := range reftiles {
 		reftile := tileVariant[libref]
-		coverage := int64(0) // number of ref bases that are called in genomes -- max is len(reftile.Sequence)*len(cgs)*2
+		tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
 		for cgidx, cg := range cgs {
 			for phase := 0; phase < 2; phase++ {
 				if len(cg.Variants) <= int(libref.Tag)*2+phase {
@@ -331,6 +331,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
 				if variant == 0 {
 					continue
 				}
+				tagcoverage++
 				genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
 				if variant == libref.Variant {
 					continue
@@ -362,7 +363,6 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
 					}
 					varslice[cgidx*2+phase] = v
 				}
-				coverage += int64(len(reftile.Sequence))
 			}
 		}
 		refpos += len(reftile.Sequence) - taglen
@@ -400,7 +400,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
 			}
 			thickend := refpos
 			// coverage score, 0 to 1000
-			score := 1000 * coverage / int64(len(reftile.Sequence)) / int64(len(cgs)) / 2
+			score := 1000 * tagcoverage / len(cgs) / 2
 			fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
 				seqname, tilestart, tileend,
 				libref.Tag,
diff --git a/pipeline_test.go b/pipeline_test.go
index 44440962a9..4dd544d813 100644
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -126,12 +126,12 @@ chr2	471	GG	AA	0/1	0/0
 	c.Check(err, check.IsNil)
 	c.Logf("%s", string(bedout))
 	c.Check(string(bedout), check.Equals, `chr1 0 248 0 500 . 0 224
-chr1 224 372 1 250 . 248 348
-chr1 348 496 2 0 . 372 472
-chr1 472 572 3 0 . 496 572
-chr2 0 248 4 750 . 0 224
-chr2 224 372 5 0 . 248 348
-chr2 348 496 6 500 . 372 472
-chr2 472 572 7 0 . 496 572
+chr1 224 372 1 1000 . 248 348
+chr1 348 496 2 1000 . 372 472
+chr1 472 572 3 1000 . 496 572
+chr2 0 248 4 1000 . 0 224
+chr2 224 372 5 750 . 248 348
+chr2 348 496 6 1000 . 372 472
+chr2 472 572 7 1000 . 496 572
 `)
 }
-- 
2.30.2